Emma-- so, so many ideas here. For starters, a question: does your family have Arabic, particularly Lebanese, heritage? I noted the Christian names Yusuf and Yaqub, as well as many French-variant saints' names. Some of the suggestions I'm making below will be partially based on that assumption, so please let me know if I'm wrong.

Personally, I think Cy feels incomplete. It's also homonymous with 'sigh,' which isn't an over-flattering association for a boy.

Re: Welsh CY- names: as noted, in Welsh these names all have the starting sound 'kuh.' There are some lovely beauties there, but it would be a bit contrived to nickname 'sigh' from Cynan, 'Kuhn-nan.'

For many reasons, I want to second Mischa's suggestion of Cyprian. It's saintly, French (well, Cyprien is), Arabic, and perhaps uniquely honors your father the arborist by its connection to the cypress tree.

Cyril-- an ancient, venerable, saintly, uncommon-but-familiar name, also given by Arabic-speaking Christians.

Cyriac-- prn with a hard C; from Greek Kyriakos, 'lord.' there are more than 25 St Cyriacs. It almost seems like a portmanteau of Cyrano de Bergerac.

Cystennin: not sure how wearable this really is, but it's the Welsh form of Constantine.

Cyran: another hard C, this is the trim original version of Cyrano. I think it's trendy -an ending sound makes it ate wearable, we still distinctive.

Hey Blade. Thank you thank you. No, no Arabic heritage, sadly. Love the sounds of that language, amazed by the culture.. though I haven't done any traveling in that part of the world, or in Cyprus for that matter. I don't think we'll end up using a name like Yusef or Yaromir, Yaqub, Lafcadio, Caelius... Just wanted to put them out there because I find them beautiful. I do think the sound of Cyprian is luscious, but it really sounds like an adjective to me. Tree names feel more vibrant to me than place names. I spent some time in Tibet, but most Tibetan names sound really contrived for a white Brooklyn kid. Nature names too I suppose, but that's non-negotiable! Cy... I hear what you're saying about the word "sigh," but it doesn't bother me. I'm just not sure if I've found a longer Cy-name or a C.Y. combination that I love as much as Cy. Cypress - love the tree, but not sure if "press" adds much to Cy. Husband likes that one. Agree with you about the Welsh Cs.
As for the saints' names - No not religious. I love the rituals and the poetry of religion, but I'm pretty groundless in that regard. Husband is decidedly more down-to-earth, likes names that don't take themselves too seriously.
First heard the name Cy on Cy Twombly, who I love. His full name isn't even close to Cy. I think it has such a coolness, like the verbal equivalent of a wink. Do you think the C.Y. initials idea is doable?

Cyril I like. I will hold onto this one and see if it sticks. I guess, it feels like a bit of an indoor-name, but I like the history and the sound.Cyriac-maniac. Cystennin-cyst. Cyran- I know an awful Kieran. Cyndeyrn- sounds tangled to me. Cybi- too cute.
Cyngar and Cydir have potential. ...Sort of. I do prefer the soft-C I think.

Backtomyroots: Thank you. I love Simon! But my husband doesn't. I think I could use it as a pet-name for a Cy. Silas- I see the appeal, but I find it a little too farmy. Makes me think of hipsters with big Amish beards. :-b

Cabot (as in the explorer, and the wild northern Bay)
Cadfan (Welsh for battle-peak)
Cadfael (as in the eponymous hero of the Ellis Peters books; a legitimate medieval Welsh name too)Caledon (ancient name for Scotland)Caradoc (derived fro Welsh cariad, 'beloved'; many herod bore the name)Casimir (a bit stronger sounding than Jaromir, with the same Slavic beauty and deep roots)Cassiel (non canonical angel)Cathal (gorgeous Irish name, though the th is prn as an H)
Chariton (masculine version of Charis)Cheyne: a definite favorite for you, as it's medieval French for 'oak'
Chivan: Tibetan names are so foreign that they're hard to wear; this is Khmer for 'life'Clovis- half-mythical king of the Franks
Colwyn: name of a lovely Welsh riverConstantine: it doesn't get any more regal; numerous good historical namesakes; uplifting meaningCorbyn: medieval French word for raven; a transferred surnameCorentin: chic in France currently; a saint; means "hurricane" in Breton
Corydon: a poetic name for the male hero-lover in French verseCorrado: romantic Italian variant of ConradCosimo/Cosmas : a saints name meaning, of course, 'universe'

As for the Ys: are you pronouncing Ywen somewhat close to Owen? The starting vowel is not like the French Yves, from what I understand. I think it's lovely, tied with Yvain for its evocative nature. I think Yves would be constantly misheard as Eve, which might create embarrassing gender confusion. Without Arabic heritage, I wouldn't consider Yusuf or Yaqub. Other ideas:

Ybarra: basque for 'valley'
Yestin: variant of Justin via Iestyn, the Welsh form
Ynyr: ancient king of GwentYsidro: gorgeous variant of Isidore

Have you considered "Schuyler" as a route to "Cy"? Crispin is lovely with nearly anything (although I'm not a fan of "Makepeace"), Cypress is another great one. "Caspar" also made me think of "Caspian", I don't know if that'd be to your liking?

Yves is very solid and I've never encountered it in the USA (I'm from Montreal), but all the Sylvans I have known have been female.